Contacts of the strand formed by residues 577 - 581 (chain B) in PDB entry 1LDK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B THR* 3.7 13.1 + - - +
570B TYR* 3.6 30.8 + - + +
571B ALA* 2.5 52.6 - - - +
574B HIS* 2.6 44.2 + - + +
575B SER* 5.0 5.7 + - - -
576B GLY* 1.3 81.3 - - - +
578B LYS* 1.3 57.9 + - - +
579B LEU* 4.3 6.9 - - + +
1034C ALA 4.0 9.2 - - - +
1035C TRP* 4.5 3.1 - - + +
1036C ASP* 3.2 4.9 - - - +
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Residues in contact with LYS 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ARG* 1.3 72.2 - - - +
579B LEU* 1.3 109.7 + - - +
580B THR* 3.9 14.7 - - + +
1033C TRP* 4.2 0.5 - - - -
1034C ALA* 3.5 29.8 + - + +
1035C TRP 4.4 2.0 - - - -
1036C ASP 2.0 40.6 - - - +
1037C ILE* 4.4 20.0 - - + -
1039C VAL* 5.4 9.3 - - + +
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Residues in contact with LEU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B THR* 4.4 24.2 - - + +
570B TYR* 3.5 51.1 - - + -
577B ARG* 4.1 8.1 - - + +
578B LYS* 1.3 128.6 + - - +
580B THR* 1.2 73.5 + - - +
581B TRP* 4.1 22.3 - - + +
1031C ALA* 5.4 2.7 - - + -
1032C LEU 4.3 3.6 - - - +
1033C TRP* 5.0 7.0 - - + -
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Residues in contact with THR 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B GLN* 4.7 14.6 - - - +
578B LYS* 3.9 17.0 - - + +
579B LEU* 1.2 91.9 - - - +
581B TRP* 1.3 67.8 + - - +
582B LEU* 4.5 2.9 - - - +
1031C ALA* 2.9 15.5 - - - +
1032C LEU* 2.9 37.4 + - + +
1033C TRP 5.0 6.1 - - - +
1034C ALA* 5.4 2.7 - - + -
1072C TRP* 6.2 3.1 - - + -
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Residues in contact with TRP 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B PHE* 3.6 35.2 - + - -
537B ILE* 3.7 27.8 - - + -
549B GLN* 4.5 9.4 - - - +
563B TYR* 4.0 47.3 - + + -
566B PHE* 4.3 26.5 - + + -
567B THR* 4.4 5.9 + - - -
579B LEU* 4.1 19.5 - - + +
580B THR* 1.3 88.8 + - - +
582B LEU* 1.3 62.0 + - - +
583B TYR* 3.0 44.1 + + + +
1027C TRP* 4.1 13.5 - + - -
1029C ALA* 4.0 9.9 - - + -
1030C VAL 3.6 1.1 - - - +
1031C ALA* 3.4 9.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il